Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)

Martini, Johannes W. R.; Gao, Ning; Cardoso, Diercles F.; Wimmer, Valentin; Erbe, Malena; Cantet, Rodolfo J. C.; Simianer, Henner

doi:10.1186/s12859-016-1439-1

Table 6 Predictive abilities on the mouse data when prior information is incorporated in the marker coding of EGBLUP. Predictive abilities when the coding for each interaction is determined based on the records of other traits

From: Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)

	G-W6W	G-W10W	G-GrowthSlope	G-BMI	G-BodyLength	G-%B220
W6W	——	0.548 ± 0.004	0.511 ± 0.004	0.507 ± 0.004	0.511 ± 0.004	0.507 ± 0.004
W10W	0.519 ± 0.005	——	0.480 ± 0.005	0.475 ± 0.005	0.475 ± 0.005	0.474 ± 0.005
GrowthSlope	0.356 ± 0.005	0.355 ± 0.005	——	0.351 ± 0.005	0.355 ± 0.005	0.351 ± 0.005
BMI	0.202 ± 0.006	0.202 ± 0.006	0.200 ± 0.006	——	0.243 ± 0.006	0.200 ± 0.006
BodyLength	0.283 ± 0.006	0.278 ± 0.006	0.281 ± 0.006	0.313 ± 0.005	——	0.276 ± 0.006
%B220	0.557 ± 0.004	0.557 ± 0.004	0.557 ± 0.004	0.556 ± 0.004	0.556 ± 0.004	——
%CD3	0.527 ± 0.004	0.527 ± 0.004	0.527 ± 0.004	0.527 ± 0.004	0.527 ± 0.004	0.562 ± 0.004
%CD4	0.500 ± 0.004	0.500 ± 0.004	0.499 ± 0.004	0.499 ± 0.004	0.500 ± 0.004	0.530 ± 0.004
%CD8	0.701 ± 0.003	0.701 ± 0.003	0.700 ± 0.003	0.700 ± 0.003	0.699 ± 0.003	0.708 ± 0.003
%CD4/CD3	0.649 ± 0.004	0.649 ± 0.004	0.648 ± 0.004	0.648 ± 0.004	0.647 ± 0.004	0.648 ± 0.004
%CD8/CD3	0.688 ± 0.003	0.688 ± 0.003	0.687 ± 0.003	0.687 ± 0.003	0.686 ± 0.003	0.687 ± 0.003
CD4Intensity	0.589 ± 0.004	0.588 ± 0.004	0.588 ± 0.004	0.588 ± 0.004	0.588 ± 0.004	0.588 ± 0.004
CD8Intensity	0.406 ± 0.005	0.405 ± 0.005	0.404 ± 0.005	0.405 ± 0.005	0.405 ± 0.005	0.404 ± 0.005
	G-%CD3	G-%CD4	G-%CD8	G-%CD4/CD3	G-%CD8/CD3	G-CD4Intensity	G-CD8Intensity
W6W	0.507 ± 0.005	0.507 ± 0.005	0.507 ± 0.005	0.507 ± 0.005	0.507 ± 0.004	0.507 ± 0.005	0.508 ± 0.005
W10W	0.475 ± 0.005	0.475 ± 0.005	0.475 ± 0.005	0.475 ± 0.005	0.475 ± 0.005	0.475 ± 0.005	0.476 ± 0.005
GrowthSlope	0.351 ± 0.005	0.351 ± 0.005	0.351 ± 0.005	0.351 ± 0.005	0.351 ± 0.005	0.351 ± 0.005	0.351 ± 0.005
BMI	0.200 ± 0.006	0.200 ± 0.006	0.201 ± 0.006	0.201 ± 0.006	0.201 ± 0.006	0.200 ± 0.006	0.202 ± 0.006
BodyLength	0.276 ± 0.006	0.276 ± 0.006	0.276 ± 0.006	0.276 ± 0.006	0.276 ± 0.006	0.276 ± 0.006	0.277 ± 0.006
%B220	0.588 ± 0.004	0.582 ± 0.004	0.570 ± 0.004	0.557 ± 0.004	0.557 ± 0.004	0.556 ± 0.004	0.558 ± 0.004
%CD3	——	0.569 ± 0.004	0.550 ± 0.004	0.527 ± 0.004	0.527 ± 0.004	0.527 ± 0.004	0.527 ± 0.004
%CD4	0.545 ± 0.004	——	0.504 ± 0.004	0.511 ± 0.004	0.510 ± 0.004	0.500 ± 0.004	0.499 ± 0.004
%CD8	0.714 ± 0.003	0.702 ± 0.003	——	0.722 ± 0.003	0.726 ± 0.003	0.700 ± 0.003	0.7 ± 0.003
%CD4/CD3	0.649 ± 0.004	0.656 ± 0.004	0.672 ± 0.004	——	0.685 ± 0.003	0.649 ± 0.004	0.649 ± 0.004
%CD8/CD3	0.688 ± 0.003	0.694 ± 0.003	0.714 ± 0.003	0.721 ± 0.003	——	0.687 ± 0.003	0.687 ± 0.003
CD4Intensity	0.588 ± 0.004	0.589 ± 0.004	0.589 ± 0.004	0.589 ± 0.004	0.588 ± 0.004	——	0.595 ± 0.004
CD8Intensity	0.403 ± 0.005	0.403 ± 0.005	0.403 ± 0.005	0.405 ± 0.005	0.404 ± 0.005	0.414 ± 0.005	——

G-W6W means that the relationship matrix was constructed under the use of the pre-corrected residuals of the trait W6W. Bold numbers indicate predictive abilities higher than that of all previously used methods for this trait

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